From f8e07ae39d5fe14ff497ef66456aaeb7aeea382b Mon Sep 17 00:00:00 2001
From: Philipp Weiler <weiler.philipp@gmail.com>
Date: Wed, 31 May 2023 16:50:09 -0400
Subject: [PATCH] Deprecate `log1p` (#1067)

* Deprecate `log1p` in favor of Scanpy's implementation

* Update unit tests relying on `log1p`

---------

Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com>
---
 scvelo/preprocessing/utils.py     | 19 ++++++++++---------
 tests/preprocessing/test_utils.py |  4 ++--
 2 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/scvelo/preprocessing/utils.py b/scvelo/preprocessing/utils.py
index 4ff8dfd6..cea850c4 100644
--- a/scvelo/preprocessing/utils.py
+++ b/scvelo/preprocessing/utils.py
@@ -5,8 +5,6 @@
 from scipy.sparse import issparse
 from sklearn.utils import sparsefuncs
 
-from anndata import AnnData
-
 from scvelo import logging as logg
 from scvelo.core import get_initial_size, get_size, multiply, set_initial_size, sum
 
@@ -587,14 +585,17 @@ def log1p(data, copy=False):
     -------
     Returns or updates `adata` depending on `copy`.
     """
-    adata = data.copy() if copy else data
-    X = (
-        (adata.X.data if issparse(adata.X) else adata.X)
-        if isinstance(adata, AnnData)
-        else adata
+    warnings.warn(
+        "`log1p` is deprecated since scVelo v0.3.0 and will be removed in a "
+        "future version. Please use `log1p` from `scanpy.pp` instead.",
+        DeprecationWarning,
+        stacklevel=2,
     )
-    np.log1p(X, out=X)
-    return adata if copy else None
+
+    from scanpy.pp import log1p as scanpy_log1p
+
+    res = scanpy_log1p(data, copy=copy)
+    return res if copy else None
 
 
 def filter_and_normalize(
diff --git a/tests/preprocessing/test_utils.py b/tests/preprocessing/test_utils.py
index 43e4708d..718aa2bd 100644
--- a/tests/preprocessing/test_utils.py
+++ b/tests/preprocessing/test_utils.py
@@ -2321,7 +2321,7 @@ def test_pancreas50obs(self, capfd, pancreas_50obs):
             )
         )
         assert pancreas_50obs.var.columns.equals(pd.Index(["gene_count_corr"]))
-        assert [*pancreas_50obs.uns] == ["pca", "neighbors"]
+        assert [*pancreas_50obs.uns] == ["log1p", "pca", "neighbors"]
         assert [*pancreas_50obs.obsm] == ["X_pca"]
         assert [*pancreas_50obs.varm] == ["PCs"]
         assert [*pancreas_50obs.layers] == ["spliced", "unspliced", "Ms", "Mu"]
@@ -2373,7 +2373,7 @@ def test_dentategyrus50obs(self, capfd, dentategyrus_50obs):
             )
         )
         assert dentategyrus_50obs.var.columns.equals(pd.Index([]))
-        assert [*dentategyrus_50obs.uns] == ["pca", "neighbors"]
+        assert [*dentategyrus_50obs.uns] == ["log1p", "pca", "neighbors"]
         assert [*dentategyrus_50obs.obsm] == ["X_pca"]
         assert [*dentategyrus_50obs.varm] == ["PCs"]
         assert [*dentategyrus_50obs.layers] == [